is there any problem with changing the shape of the baffle such as making the top flat?
That will add some surface reflections. Not an amount that is detrimental. It would be subtle, but not in a positive way.
When looking at the original plans for the Super V the plate below the P driver which the crossover goes under is angled and with the flat pack it is flat and then curves down in the back. Does the shape of this area make any difference?
All just an effort to minimize the effect of their being a flat surface there. Slanting it away from the driver helps.
Also, how far down the front of the baffle matters?
Everything has some effect.
Does the speaker care if the bow tie is removed or the area below that?
The bow-tie is just to separate the upper and lower grills. It can be removed. I would not increase that area in that region though. The driver still needs to be near ear level.
And would it matter if the top baffle section is separated by an open space say an inch from the lower subwoofer section?
Yes, that would alter the front to back separation.